Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::frag_picker::quota::SecondaryStructurePool Class Reference

represents a single pool used by quota selector More...

#include <SecondaryStructurePool.hh>

Public Member Functions

 SecondaryStructurePool (Size, std::string, char, utility::vector1< Size > &, utility::vector1< Real > &, Real, Size, Size)
 Creates a pool of a given size and name. More...
 
char get_ss_type () const
 
virtual ~SecondaryStructurePool ()
 
virtual Size total_size () const
 Says how many fragments (in total) may fit into this pool. More...
 
virtual Size current_size () const
 Says how many fragments are currently in this pool. More...
 
virtual Size size_left () const
 Says how many fragments can still be inserted into this pool. More...
 
virtual bool could_be_accepted (ScoredCandidate) const
 
virtual void push (ScoredCandidate candidate)
 Push a fragment candidate into the container. More...
 
virtual bool add (ScoredCandidate)
 Insert a fragment candidate to the container. More...
 
void clear ()
 removes all candidates from the container More...
 
Size count_candidates (Size) const
 Check how many candidates have been already collected for a given position. More...
 
Size count_candidates () const
 Check how many candidates have been already collected for all positions. More...
 
Size query_length () const
 Check the size of query sequence that this object knows. More...
 
void insert (Size, CandidatesCollectorOP collector)
 Inserts candidates from another Collector for a give position in the query Candidates may or may not get inserted depending on the candidate. More...
 
ScoredCandidatesVector1get_candidates (Size)
 Returns all the candidate in this pool. More...
 
void resize (Size new_size)
 
void print_report (std::ostream &, scores::FragmentScoreManagerOP) const
 Describes what has been collected. More...
 
virtual void set_fraction (Real new_fraction)
 Sets the fraction of this quota pool in the entire population of fragments. More...
 
virtual Real quota_score (ScoredCandidate candidate) const
 provides the score for a candidate that was used to sort a quota pool More...
 
- Public Member Functions inherited from protocols::frag_picker::quota::QuotaPool
 QuotaPool (std::string pool_name, Real quota_fraction)
 Creates a pool of a given size and name. More...
 
virtual ~QuotaPool ()
 
std::string const & get_pool_name () const
 returns the name assigned to this quota pool More...
 
virtual void show_availability (std::ostream &where) const
 prints information on which fragments can be accepted by this pool and how many of them More...
 
Real get_fraction () const
 returns the fraction of this quota pool in the entire population of fragments More...
 

Private Attributes

Size total_size_
 
Size this_size_
 
char ss_type_
 
utility::vector1< Sizecomponents_
 
utility::vector1< Realweights_
 
BoundedQuotaContainerOP storage_
 
Size buffer_factor_
 

Detailed Description

represents a single pool used by quota selector

Constructor & Destructor Documentation

protocols::frag_picker::quota::SecondaryStructurePool::SecondaryStructurePool ( Size  total_size,
std::string  pool_name,
char  ss_type,
utility::vector1< Size > &  which_components,
utility::vector1< Real > &  weights,
Real  fraction,
Size  n_scores,
Size  buffer_factor = 5 
)

Creates a pool of a given size and name.

Parameters
size- total number of fragments from all the pools at a given position
name- name assigned to this pool. This in general may be any string that later allows one control pool's behavior from a flag file
ss_type- what is the type of secondary structur this pool is accepting
score_components_id- which scores will be used to sort this pool
weights- weights for the scores that in general may be different than these used for fragment picking
fraction- fraction of this pool in the entire population
total_size- how many fragments will be selected (in total in all pools)
name- name assigned to this pool. This in general may be any string that later allows one control pool's behavior from a flag file
ss_type- what is the type of secondary structur this pool is accepting
fraction- fraction of the total number of fragments that goes into this pool

References buffer_factor_, components_, ss_type_, storage_, this_size_, total_size(), total_size_, protocols::frag_picker::quota::trSecondaryStructurePool, and weights_.

protocols::frag_picker::quota::SecondaryStructurePool::~SecondaryStructurePool ( )
virtual

Member Function Documentation

bool protocols::frag_picker::quota::SecondaryStructurePool::add ( ScoredCandidate  candidate)
virtual

Insert a fragment candidate to the container.

Implements protocols::frag_picker::CandidatesCollector.

References ss_type_, and storage_.

void protocols::frag_picker::quota::SecondaryStructurePool::clear ( )
inlinevirtual

removes all candidates from the container

Implements protocols::frag_picker::quota::QuotaPool.

References storage_.

bool protocols::frag_picker::quota::SecondaryStructurePool::could_be_accepted ( ScoredCandidate  candidate) const
virtual
Size protocols::frag_picker::quota::SecondaryStructurePool::count_candidates ( Size  ) const
inlinevirtual

Check how many candidates have been already collected for a given position.

Detailed: This is a very special case - collector will be used only for a given position.
Thus it returns the total number of inserted candidates, as count_candidates() does

Implements protocols::frag_picker::CandidatesCollector.

References current_size().

Size protocols::frag_picker::quota::SecondaryStructurePool::count_candidates ( ) const
inlinevirtual

Check how many candidates have been already collected for all positions.

Implements protocols::frag_picker::quota::QuotaPool.

References current_size().

virtual Size protocols::frag_picker::quota::SecondaryStructurePool::current_size ( ) const
inlinevirtual

Says how many fragments are currently in this pool.

Implements protocols::frag_picker::quota::QuotaPool.

References storage_.

Referenced by count_candidates(), print_report(), and size_left().

ScoredCandidatesVector1& protocols::frag_picker::quota::SecondaryStructurePool::get_candidates ( Size  )
inlinevirtual

Returns all the candidate in this pool.

Implements protocols::frag_picker::CandidatesCollector.

References storage_.

char protocols::frag_picker::quota::SecondaryStructurePool::get_ss_type ( ) const
inline

References ss_type_.

void protocols::frag_picker::quota::SecondaryStructurePool::insert ( Size  ,
CandidatesCollectorOP  collector 
)
inlinevirtual

Inserts candidates from another Collector for a give position in the query Candidates may or may not get inserted depending on the candidate.

Implements protocols::frag_picker::CandidatesCollector.

References c, l, storage_, and utility_exit_with_message.

void protocols::frag_picker::quota::SecondaryStructurePool::print_report ( std::ostream &  out,
scores::FragmentScoreManagerOP   
) const
virtual
virtual void protocols::frag_picker::quota::SecondaryStructurePool::push ( ScoredCandidate  candidate)
inlinevirtual

Push a fragment candidate into the container.

Implements protocols::frag_picker::quota::QuotaPool.

References storage_.

Size protocols::frag_picker::quota::SecondaryStructurePool::query_length ( ) const
inlinevirtual

Check the size of query sequence that this object knows.

Detailed: This is a very special case - collector will be used only for a given position and it does NOT
know the tolal size. Thus it returns always 0

Implements protocols::frag_picker::CandidatesCollector.

virtual Real protocols::frag_picker::quota::SecondaryStructurePool::quota_score ( ScoredCandidate  candidate) const
inlinevirtual

provides the score for a candidate that was used to sort a quota pool

Detailed: This base class returns the most recent total score for a fragment

Reimplemented from protocols::frag_picker::quota::QuotaPool.

References components_, and weights_.

void protocols::frag_picker::quota::SecondaryStructurePool::resize ( Size  new_size)
inline

References buffer_factor_, and storage_.

virtual void protocols::frag_picker::quota::SecondaryStructurePool::set_fraction ( Real  new_fraction)
inlinevirtual

Sets the fraction of this quota pool in the entire population of fragments.

Reimplemented from protocols::frag_picker::quota::QuotaPool.

References buffer_factor_, protocols::frag_picker::quota::QuotaPool::set_fraction(), storage_, this_size_, and total_size_.

virtual Size protocols::frag_picker::quota::SecondaryStructurePool::size_left ( ) const
inlinevirtual

Says how many fragments can still be inserted into this pool.

Implements protocols::frag_picker::quota::QuotaPool.

References current_size(), and total_size().

virtual Size protocols::frag_picker::quota::SecondaryStructurePool::total_size ( ) const
inlinevirtual

Says how many fragments (in total) may fit into this pool.

Implements protocols::frag_picker::quota::QuotaPool.

References storage_.

Referenced by SecondaryStructurePool(), and size_left().

Member Data Documentation

Size protocols::frag_picker::quota::SecondaryStructurePool::buffer_factor_
private
utility::vector1<Size> protocols::frag_picker::quota::SecondaryStructurePool::components_
private
char protocols::frag_picker::quota::SecondaryStructurePool::ss_type_
private
BoundedQuotaContainerOP protocols::frag_picker::quota::SecondaryStructurePool::storage_
private
Size protocols::frag_picker::quota::SecondaryStructurePool::this_size_
private
Size protocols::frag_picker::quota::SecondaryStructurePool::total_size_
private
utility::vector1<Real> protocols::frag_picker::quota::SecondaryStructurePool::weights_
private

The documentation for this class was generated from the following files: